Does your CO say anything about him having your son for Father's Day, regardless of who's custody he's in at the time? If your CO states that your ex has every Father's Day, but doesn't define how transportation would be arranged specifically for that, then you're SOL. Transportation would then have to be agreed upon by the both of you, unless you go back to court and have it ordered. If your CO states that you pay for all transportation regardless, I think you're SOL on that one, too. As for if he does book a flight, it would just be a matter of calling the airline to find out if there's a return flight, but I would do that BEFORE you put the child on a plane.
Is your order somewhat new, in that this is the first summer you are doing this? From the sound of it, it sounds like there might be some 'holes' in your final judgement regarding transportation. And it's possible that the only way to close those holes is to go back to court for clarification. May be pricey, but you have to weigh that against how much you might end up spending on transportation completely and over the long haul. If you do manage to agree on trans. for this summer, who's to say the same issue won't come up again next summer, or the next?
As far as talking to your ex about it, tell him that since it's ordered that you have this time, anything he does counter to that would be considered contempt. And if that also means you will be out the cost of the ticket (which certainly is a lot of money), you would be forced to file contempt and asking for the cost of the ticket. You might also tell him that, if the shoe was on the other foot, you would expect him to react the same way.
Good luck with this. We did LD parenting for about 8 years...I know how difficult and expensive it can be. But I also know that if you can't communicate and cooperate with the other parent, it almost makes it impossible